thursday, march 2, 2017 8:30am – 4:30pm usda … · stakeholder presentations for the usda‐ocs...

Stakeholder presentations for the USDA‐OCS March 2, 2017 public listening session “Visioning of United States Agricultural Systems for Sustainable Production”

Visioning of United States, (U.S.) Agricultural Systems for Sustainable Production Stakeholder Listening Session Meeting

Thursday, March 2, 2017 8:30am – 4:30pm USDA South Building Cafeteria

Welcome! • Bathrooms between cafeteria and security entrance • Safety – nearest exit towards south side of building • WiFi access USDA‐Guest

Name: patio Password: test123

• Teleconference and WebEx participants • May take questions from WebEx chat

• Public listening session – will attempt to record session • All comments, written and oral may be used in any form (including

edited for length, in print, web, etc.)



Enter Here (wing 3) Smithsonian

National Mall Metro

Cafeteria bathrooms

Meeting

Emergency Exit

The comments and opinions expressed herein are those of individual stakeholders made publicly and do not necessarily represent those of USDA

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Welcome! • Research discussion, what avenues of science can hold

• In no way connected to policy • Focused on longer‐term future • We want to acknowledge there are areas of disagreement without

squishing them, but try to move on to get to consensus areas. • Sara Scherr is helping to facilitate because of her expertise in these

activities



Structure • Few invited presentations • Stakeholder presentations – somewhat grouped • Pooled time for questions and discussion • Breakout sessions – questions in slides, email and back of agenda

• Notecards are for questions comments, etc. to go in written record • Use easel pads for group discussions


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Office of the Chief Scientist • Ensures the Chief Scientist is the leading communicator

of USDA Science nationally & internationally • Advises the Secretary & Departmental Leadership • Ensures a Department‐wide culture of science‐based

decision making for science policy • Raises the visibility of USDA Science • Institutes, maintains, & enhances USDA’s Scientific

Integrity Policy



Dr. Ann Bartuska

Acting Under Secretary, Research, Education, and Economics

USDA


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Brainstorming Approach – Beginning a Conversation • Focus on agricultural production systems 50 years from now • Consider how to integrate basic scientific discoveries and technology • Please be

• Open minded • Visionary • Bold in new ideas • Use systems thinking – across silos, disciplines, and commodities

What is something you wish people understood better, that would make your area of agriculture more successful?



# 1 Dr. Elise Golan

Director for Sustainable Development Office of the Chief Economist

USDA

https://www.usda.gov/oce/sustainable/definitions.htm


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http://www.usda.gov/oce/sustainable/definitions.htm





https://www.usda.gov/oce/sustainable/definitions.htm

Farm Bills: The 1977 and 1990 “Farm Bills” describe sustainable agriculture as an integrated system of plant and animal production practices having a site‐specific application that will, over the long term: • satisfy human food and fiber needs; • enhance environmental quality and the natural resource base upon which the

agricultural economy depends; • make the most efficient use of nonrenewable resources and on‐farm resources

and integrate, where appropriate, natural biological cycles and controls; • sustain the economic viability of farm operations; • enhance the quality of life for farmers and society as a whole.



# 2 Dr. Charles Walthall

National Program Leader Natural Resources and Sustainable Agricultural

Systems Agricultural Research Service

USDA‐ARS


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Precision Agriculture

Walthall –USDA ARS“Efficiency”

Remote Sensing

Walthall –USDA ARS“Condition & Capacity”

The comments and opinions expressed herein are those of individual stakeholders made publicly and do not necessarily represent those of USDA 6


“Decision Support”“Options”

GxExM

Walthall –USDA ARS

• Lots of data – analysis? • “Big Data” tools?• Models for “what if?” scenarios

• Potential not realized; adoption rates?• R&D: Roles for public funding, industry

Dr. Mitch Tuinstra

Professor and Wickersham Chair of Excellence Department of Agronomy

Purdue University

DOE ARPA‐E



# 3



MULTI-SCALE ANALYSIS OF FIELD-GROWN CROPS TO ENHANCE CROP IMPROVEMENT

AND PRODUCTION RESEARCH Mitch Tuinstra1, Christopher Boomsma1, Javier Ribera1, Yuhao Chen1, Fangning He1, Weifeng Xiong1, Zhou Zhang1, Addie Thompson1, Karthikeyan Natesan Ramamurthy2, Aurelie Lozano2, Naoki Abe2, Ayman Habib1, Edward Delp1, Larry Biehl1, Michael Leasure1, Keith Cherkauer1, Clifford Weil1, and Melba Crawford1

1Purdue University, West Lafayette, IN March 2 listening session 2IBM Research, Yorktown Heights, NY

Purdue University is an equal access/equal opportunity institution.

PRECISION PHENOTYPING – LINKING GENES TO PHENOTYPES

Environmental Genetic Adaptation Diversity

Climatic and Edaphic High-value population in Variables many crops and models

Crop Breeding Pipeline

Phenotypic Genetic

Characterization Information • Yield Potential • Genomic profiles to estimate • Abiotic Stress Adaptation genetic relationships • Disease Resistance • Gene-based markers • Plant Architecture • Pedigrees • Quality

A BIG “Big Data” Challenge and Opportunity


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• •

PRECISION PHENOTYPING THE CONVERGENCE OF BIOLOGY × ENGINEERING × COMPUTER SCIENCE

Crop Genetic Gain

Genomics and Resilience Cloud

Plant, Animal, Human Distributed Database and Microbial Big Data with Remote Access

Analysis

Gene and Trait Phenotype = Genotype × Environment x Management Crop Prediction Associations Yield

Physiology Algorithms Composition

Environment Stress

Phenomics Analytics Phenotype Reference High Performance

Standards (Lab & Field) Roots Soil Data Pipelines Microbiome Innovations Enhance:

Water Nutrients • Crop Breeding • Agronomic Research

High Resolution • Precision Farming AI-Machine Crop Phenotypes • Land Management Learning

Resource Conservation Market Connectivity

Sensors Robotics Plant, Root, Soil, Microbial High Throughput Field Deployable,

and Environmental Field Data Acquisition Scalable and Economical

SMARTER AGRICULTURE MORE EFFICIENT CROP IMPROVEMENT AND AGRONOMIC RESEARCH PLATFORMS

Smarter Agriculture™ platforms will provide plant science researchers with a data management infrastructure that will organize data from many disparate streams in a cohesive way for more robust analysis in a secure framework that allows collaboration, data reuse and publication.


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AUTOMATED CROP PHENOTYPING PLATFORMS DOE ARPA-E TERRA PROGRAM FOR HIGH-THROUGHPUT SORGHUM PHENOTYPING

Purdue University • Larry Biehl: information technology • Christopher Boomsma: crop physiology, phenotyping • Keith Cherkauer: UAV technology, remote sensing • Melba Crawford: remote sensing, machine learning • Edward Delp: image and video processing • David Ebert: visual analytics • Ayman Habib: digital photogrammetry, LiDAR • Michael Leasure: UAV technology and operations • Addie Thompson: quantitative genetics • Mitch Tuinstra: plant breeding, genetics University of • Clifford Weil: plant genomics Queensland

IBM • Naoki Abe: machine learning, data mining • Upendra Chitnis: data warehousing, spatio-temporal databases • Aurelie Lozano: high-dimensional data analysis Applanix • Peder Olsen: machine learning • Karthikeyan Natesan Ramamurthy: machine learning Industry

AgReliant Genetics University of Queensland Partners • Scott Chapman: crop modeling, phenotyping • Graeme Hammer: crop modeling John Deere

DATA ACQUISITION PLATFORMS REMOTE SENSING TECHNOLOGY



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GROUND VALIDATION STUDIES IN SITU DATA ACQUISITION

Step-wise ortho-rectification

x, y, and z accuracy ≈ 2 cm

GEOMETRIC CORRECTION DATA PROCESSING

System Calibration

RGB Image Data Processing

Hyperspectral Image Data Processing

LiDAR Data Processing GNSS/INS Integration



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−1

σ 2

PLANT LOCATION AND SPACING FEATURE EXTRACTION AND LEARNING

γ (x ) = 1 M

∑ D (x ) + 1 x − µ 2

p m p p

m=0 p −1

p

Initialize plant positions

randomly

Select next

plant p

Compute γ(xp) for candidate

positions around xp

Yes No

?

Could plant p move?

Move xp

to pixel with lowest γ(xp) for candidate

R

PLANT LOCATION AND SPACING FEATURE EXTRACTION AND LEARNING

Spacing mean (cm)

Date: July 21, 2016 Sensor: Sony Alpha 7R UAV: DJI S1000+ Altitude: 44 m Velocity: 5 m s-1

Overlap: 70%

34 32 28 29 32 25 26 30 36 33 26 32

28 17 8 11

13 11 11

19 24

10 13 12

Spacing standard deviation (cm)



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LEAF NUMBER FEATURE EXTRACTION AND LEARNING

Leaf edge detection

Leaf edge detection

Leaf segmentation

Leaf segmentation

LEAF NUMBER FROM CUMULATIVE COUNTS FEATURE EXTRACTION AND LEARNING

3500

20150615 20150626

3000 20150706 20150715

2500

2000

1500

1000

500

0 4000 4050 4100 4150

plot number

Average 20150615 20150626 20150706 20150715

Accumulated Leaf counts

271.9 802.8 1431.7 2146

leaf

cou

nts



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CANOPY COVER FEATURE EXTRACTION AND LEARNING

Date: July 21, 2016 Sensor: Sony Alpha 7R UAV: DJI S1000+ Altitude: 44 m Velocity: 10 m s-1

Canopy cover mean (%) 26 24 16 10 6 25 22 23 13 21 25 14

51 63 45 42

44 20 42

49 53

29 28 38

Canopy cover CV (%) Low High

PLANT HEIGHT AND LODGING FEATURE EXTRACTION AND LEARNING

Sensor: Sony Alpha 7R UAV: DJI S1000+ Altitude: 55 m Velocity: 10 m s-1

Overlap: 70%

August 9, 2016 215 m 220 m

August 17, 2016



PREDICTIVE LEARNING LATENT FEATURE EXTRACTION

Multi-modal data provide a unique challenge for data fusion and phenotype prediction.

Raw spectra, spectral indices, EMAP, height histograms

Phenotypic trait prediction performance

Feature fusion and predictive learning

Phenotype RMSE R2 Bias (%)

Plant height 32.44 cm 0.80 3.05

Stem diameter 3.01 mm 0.52 0.50

Stem volume (DE) 80.56 cm3 0.23 5.27

Stem volume (PE) 71.01 cm3 0.25 6.38

GENE DISCOVERY STUDIES – PLANT HEIGHT GENOME WIDE ASSOCIATION STUDIES

Manhattan plot for height histogram features Chr 7



MOBILIZING RESEARCH FOR DEVELOPMENT ENHANCE FOOD SECURITY

Automated phenotyping technologies based on airborne and ground- based sensor systems must be developed that will enable gene discovery and optimization of crop varieties and production systems for food production.

Nutritional Deficiencies Map

Automated phenotyping

ROOTS RHIZOSPHERE OBSERVATIONS

OPTIMIZING TERRESTRIAL SEQUESTRATION

OBJECTIVES: 1. CARBON ASSIMILATION (CO2 EMISSIONS MITIGATION= SOIL ORGANIC MATTER)

2. NUTRIENT ACQUISITION (N2O EMISSIONS REDUCTION = FERTILIZER EFFICIENCY)

3. WATER PRODUCTIVITY (RESOURCE USE EFFICIENCY = CLIMATE RESILIENCE)



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# 4 Laurie‐Ann Flanagan

Executive Vice President D.C. Legislative and Regulatory Services, Inc.

Sara Scherr, Ph.D. moderating

The Role of Biopesticides and Biostimulants in Sustainable

Agriculture Systems

Prepared for USDA’s Visioning of U.S. Agriculture Systems for Sustainable Production Listening Session

March 2, 2017



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What are Biopesticides? Biopesticides are reduced risk pesticides that are naturally derived or synthetic equivalents of natural materials such as animals, plants, bacteria, fungi and certain minerals, generally posing little risk to humans or the environment. Biopesticides:

• Allow conventional growers to integrate reduced risk pesticides into their pest

management program • Play an important role in public health protection • Are important components of IPM Programs • Allow greater flexibility when harvesting due to short restricted entry intervals • Are effective resistance management tools because of their alternative modes of

actions • Can be used as residue‐management tools • Allow organic growers to control pests while maintaining their certified status

What are Biostimulants?

Biostimulants are derived from natural or biological sources such as bacterial or microbial inoculants, biochemical materials, amino acids, humic acids, fulvic acid, seaweed extract and other similar materials. These products improve agricultural sustainability and soil health. Biostimulants:

• Enhance plant growth and development • Improve the efficiency of plant nutrients, as measured by either improved

nutrient uptake or reduced nutrient losses to the environment, or both; and/or

• Act as soil amendments, with demonstrated ability to help improve soil structure, function or performance and thus enhance plant response



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Policies that encourage the development and use of new biopesticide and

biostimulant products will enhance the sustainability and productivity of both

conventional and organic agriculture over the next several decades

Suggested Policies to Further the Development and Adoption of Biopesticides and Biostimulants

• Increase funding for USDA’s Minor Crop Pest Management (IR‐4) Program’s Biopesticide and Organic Support Program and other research programs related to pest control

• Add an input provider’s seat to the National Organic Standards Board • Clarify the definition of biostimulants and consistently apply that definition

across all associated regulatory structures • Encourage the use of biopesticides and biostimulants in USDA Conservation

Programs • Task the USDA BioPreferred Program and BPIA to develop criteria for

certifying biopesticides as USDA BioPreferred



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# 5 Tom Martin

Chairman & CEO EnviroCirc

Tom Martin CEO

™



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Circular Farm Green Bond • 3 percent, 20‐year, $10B Green Bond • Save Family Farms – Kids return to farming

– Fund organic farm transition ‐ Partner with lenders – Respected underwriter & 3rd party verification – Governed by ICMA Green Bond Principles – Tap CERES sustainability‐focused fund managers – Issuance requires verifiable Enviro‐benefits – Model delivers EnviroHealth improvements, profitably – Lake Erie & Lake Champlain Eutrophication solution – Circular Farm Agrarian Communities – new paradigm

EnviroCirc™ Proven Via NRCS Field Trials On 11 Dairy/Swine Farms. CIG Grant # NRCS 69‐3A75‐0‐123

Aerobic Treatment Of Manure Lagoons Showing Environmental & Economic Benefits With Eco‐Service System Paybacks



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• Makes Manure Disappear • Transformed to 99% true liquid EnviroFertilizer™ • Odor/Pathogen‐free SOLUTION enables:

– Precision Fertigation via Pivot, Drip or SDI – Cover Crop + No‐Till + EnviroFertilizer™ = – Elimination of Chemical Fertilizer – Transform farmland to Organic @Scale – Double Value

Tom Martin ‐ CEO EnviroCirc.wordpress.com 781‐686‐2133 [email protected]


mailto:[email protected]


Rebecca A. Dudley

Chairman & CEOEnviroCirc



# 6



We talked to farmers across the US – from Oregon, Kansas, Iowa, Michigan, and Kentucky.

They’re using key technologies like connected crop services, yield map analysis, droning, and precision irrigation.

COPYRIGHT 2017 ACCENTURE. ALL RIGHTS RESERVED. 47

THE HAS SHIFTED TOWARDS RURAL AMERICAWhat drives rural America?What constrains rural America?

How are new, digital technologies transforming farming decisions and operations?


70% access high-speed internet.

73% use digital technology in day-to-day decisions.

84% expressed willingness to interact with USDA online.

FARMERS WANT TO ENGAGE,




THEY NEED TO BE FIRST.What is the return on investment for engagement in digital?

Why isn’t the digital farming experience intuitive and easy?

How can they be sure that their data is secure?

USDA CAN .

Focus on digital solutions that align to rural sector and farming needs.

Connect datafrom disparate platforms, and help users connect in.

Build on connected datafor insights and enhanced analytics for predictive modeling.

AND HERE’S

Rural Development: Building telecommunications

Across USDA: New farming technologies

Create digital solutions that connect data sources – from sensors in the field to weather prediction

Enable farmers easy, plug-and-play tools for predictive analytics

Elaine Turville, Managing Director, Human [email protected]

Molly Bauch, Technology Strategy Manager, AFS [email protected]

Danny Cohanpour, Management Consulting Senior Analyst, AFS [email protected]

Rebecca Dudley, Management Consulting Senior Analyst, AFS [email protected]







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# 7 Matthew Lange, PhD

Research Food and Health Informatician Principal Investigator, IC3‐FOODS

Associate Director, Initiative for Wireless Health & Wellness

UC Davis and UC Davis Health System

IC3-FOODS: International Conference - Consortium - Center for

Food Ontology Operability Data and Semantics

@IC3FOODS ASSEMBLING‐DESIGNING‐BUILDING THE ONTOLOGICAL AND COMPUTATIONAL INFRASTRUCTURE FOR The Internet of Food

Semantic Web & Internet of Food Food Systems, Food, Eating, Drinking, & Health Enabling Decision support for:

Food Production, Processing, Safety, Security Environmental Sustainability

Personalized Products Wellness & Happiness

@mateolan Matthew Lange, PhD [email protected]




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Semantic Web & Internet of Food A common language, infrastructure, & pre-competitive platform to operationalize vast data along:

Env⇔Ag⇔Food⇔Diet⇔Health

@IC3FOODS www.ic-foods.org #InternetOfFood




Pervasive sensors: window into human behavior





http://www.ic-foods.org/


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© Matthew Lange, PhD

Semantic Web of Food ystems, Food, & Health

Fletcher, A and Lange, M Ontology of food processing

and the Regents of the University of California

Ontology of Food Processing

S

From Precision Ag P to Precision Health *-omics R E

E R Behavior Activity Sleep Stress Sensing E I C S

R D N O O Sensory Meals Assessing E U N M N Diets Habits Rituals S C O M A

E V E Micro- Tracking A

A A N L Processing

structure Bio-

Flavor R T T D I

availability Mapping C

I I A Z Location Inputs Labor Sustainability H

O O T A N N I T Optimizing O I Microclimate Soil Water Sustainability N O Predicting N

IDENTITY & AGGREGATION

QUANTITATION & STORAGE COMBINATORICS VISUALIZATION & ANALYSIS & INTERACTION

May 8-11,FOOD

2017AG & FOOD PRODUCTION

ENERGY & ENVIRONMENT

Nov 7 9 2016

IC-FOODS@ SeedsHE&ALTH

ChipsEATING

IC3‐FOODS International Conference ‐ Consortium ‐ Center for Food Ontology Operability Data & Semantics

ASSEMBLING‐DESIGNING‐BUILDING THE ONTOLOGICAL AND COMPUTATIONAL INFRASTRUCTURE FOR

www.ic-foods.org #InternetOfFood @IC3FOODS


http://www.ic-foods.org/


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# 8 Kristina J. Owens

Scientific Advisor & Associate Eversole Associates

The International Alliance for Phytobiomes Research: A Vision for Agriculture

Kristina Owens, Consultant On Behalf of Kellye Eversole, Executive Director

of the Phytobiomes Alliance USDA Stakeholder Meeting Washington, DC, USA 2 March 2017



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Real World Agriculture • Crop production is a complex system organized in a non-

linear manner • It is governed by multiple nonlinear interactions and multiple

environmental variables • Agriculture requires multidisciplinary systems understanding

We need a global, systems approach to elucidate, quantify, model, and potentially reverse engineer biological processes & mechanisms for their geophysical context

How? Decipher Phytobiomes

“Biome” - Site

Associated organisms

Phytobiomes Climate

Crop plants, their environment, and their associated micro- and macro-organisms.

Plants Arthropods, Other Micro- and Macroorganisms Animals and Plants

Viruses Insects Archaea Arachnids Bacteria Myriapods Amoeba Worms

Oomycetes Birds Algae Rodents Fungi Ruminants

Nematode Weeds

Soils

specific environment



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The Phytobiomes Alliance An international, nonprofit Alliance of industry, academic, and governmental partners

Vision: All farmers have the ability to use predictive and

prescriptive analytics to choose the best combination of

crop/variety, management practices, and inputs for a specific field

in a given year taking into consideration all physical (climate,

soil…) and biological conditions (microbes, pests, disease,

weeds, animals….).

Alliance Priorities • A whole genome sequence database for microbes that includes geospatial

data

• Accessible, curated strain repository for all agriculturally relevant microbes with back-up at ARS genetic resources preservation labs

• Multidisciplinary phytobiomes research coordination networks

• Standards development – sampling, storage, reference communities, reference datasets for analytical tool development

• Research linking site-specific physical & biological data for crops, forests, and grasslands

• Science to support the regulations that may exist for agricultural biologicals, including biopesticides and permitting



Thank you!

For More Information: www.phytobiomesalliance.org

Kellye Eversole [email protected]



# 9 Sara Scherr, Ph.D. Moderated Questions and Discussion Time

Laurie Flanagan Tom Martin

Rebecca Dudley Matthew Lange

Kristina J. Owens reminder: if no live comments, go to WebEx chat


http://www.phytobiomesalliance.org/





# 10 20min Break and Networking

reminder: stop and restart WebEx Recording to

reduce file size


thursday, march 2, 2017 8:30am – 4:30pm usda … · stakeholder presentations for the usda‐ocs...

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